Protease deficient caulobacter host cells

ABSTRACT

Caulobacter  optimized for use in expression of heterologous peptides as part of a hybrid  Caulobacter  S-layer protein are provided as well as methods for producing such  Caulobacter. Caulobacter  of this invention are deficient in a native  Caulobacter  protease that cleaves hybrid S-layer proteins. Also provided are  Caulobacter  libraries and methods for sorting such libraries using cell sorting technoloey such as FACS.

BACKGROUND OF THE INVENTION

The gram-negative bacterium Caulobacter elaborates a paracrystalline protein surface layer (S-layer) which covers the surface of its outer membrane (Smit, et al., 1981; 1992). The S-layer protein monomer is secreted by a Type I secretion mechanism relying upon a C-terminal secretion signal which remains attached to the rest of the protein during the secretion process (Gilchrist, et al., 1992; Bingle, et al. 1997a; and, Awram and Smit 1998). Once the protein monomer is secreted, the S-layer forms by a process of self-assembly as a hexagonal array of about 40,000 interlinked protein monomers (Nomellini, et al., 1997). Anchoring of the S-layer protein to the cell surface is dependent on a smooth lipopolysaccharide (LPS) molecule and Ca⁺² ions (Walker, et al, 1994) and involves the N-terminal portion of the S-layer monomer (Bingle, et al, 1997 a,b). The abundance, cell-surface location and geometrical packing of the S-layer protein as well as the inherent properties of Caulobacter (ease of genetic manipulation, simple growth requirements, non-pathogenic nature, and biofilm-forming characteristics) have led to the exploitation of the Caulobacter/S-layer system for biotechnology development (Smit, et al., 2000).

Through use of gene fusions encoding the C-terminal secretion signal of the S-layer monomer linked to sequences encoding a heterologous peptide, the Caulobacter/S-layer system is capable of secreting large quantities of the heterologous peptide (PCT patent applications published under No. WO 97/34000 and WO 00/49153; and, Bingle, et al., 2000). Such Caulobacter expression systems are available commercially under the trade name PurePro™ (Invitrogen, Carlsbad, Calif.). The PureProm™ system is designed for expression of “C-terminal hybrid proteins” in which a heterologous peptide is linked to the S-layer monomer C-terminal secretion signal and does not form an S-layer on the host.

The Caulobacter/S-layer system is also used for expression of heterologous peptides inserted into sites within a full-length (or nearly full-length) S-layer monomer resulting in production of what is termed herein “full-length hybrid protein”. In such cases, a sufficient portion of the N-terminal region of the S-layer monomer is present to provide anchoring of the hybrid protein to the cell surface. The C-terminal secretion signal is present to permit secretion of the hybrid protein. Various preferred sites for insertion of heterologous peptides into the S-layer protein have been reported (WO 97/34000; and, Bingle, et al., 1997(b)). The hybrid S-layer protein so produced is capable of self-assembly on the cell surface resulting in an array of hybrid S-layer protein monomers forming as an S-layer on the cell surface. In this manner, heterologous peptides may be expressed and presented on the cell surface. This technology has particular use in expression and presentation of antigens.

A phenomenon observed during the development of the Caulobacter/S-layer system was the apparent proteolytic cleavage of various hybrid proteins. This was initially observed for both C-terminal hybrid proteins and full-length hybrid proteins. No obvious site specificity was associated with this phenomenon despite monitoring the degradation of numerous modified S-layer proteins comprising different heterologous peptides of varying lengths inserted at different places in the S-layer protein monomer (Bingle, et al. 1997a,b) it has now been reported (Simion, B. et al. 2001) that smaller proteins seen contaminating preparations of C-terminal hybrid proteins are not the result of proteolytic activity but rather the result of internal translation initiation following Met residues within the heterologous or “passenger” portion of the hybrid protein. Nevertheless, the cleavage phenomenon still places limitations on the use of Caulobacter as an expression system for full length hybrid proteins, particularly when the “passenger” peptide is unknown or uncharacterized, since it would then be difficult to know if this phenomenon has affected the hybrid product.

The use of a biological system to express and display a panel or library of different peptides to assess the ability of the peptides to bind to a chosen target, has become a powerful tool for investigating interaction of cellular components (see U.S. Pat. Nos. 5,223,409 & 5,571,698). In this methodology, nucleic acids each encoding a different peptide plus a signal for display of the peptide on the outer surface of a biological system, are introduced into the system. The peptides are expressed and binding domains in the peptides are displayed on the outer surface of the biological system. The system is exposed to target molecules and those members of the system which bind target molecules are isolated and the nucleic acids amplified. Successful binding domains are then characterized. This general method of exposing a variety of peptides, each displaying a different putative binding region, is termed “panning” herein. To date, phage is the preferred biological system for use in panning methodologies. This is partly due to difficulties in the use of bacterial systems for expression and display of heterologous peptides.

SUMMARY OF THE INVENTION

It has now been discovered using studies involving full-length hybrid proteins that a protease is synthesized by Caulobacter with an unusual structural feature: the enzyme possesses a domain sharing sequence similarity with the S-layer protein monomer. This native protease is responsible for the cleavage phenomenon seen with Caulobacter expressing heterologous peptides inserted into a full-length S-layer protein.

This discovery provides the means for optimizing use of Caulobacter as a system for expression and cell-surface display of heterologous peptides and for use of such a system for expression of unknown or uncharacterized peptides with good fidelity. This facilitates the use of Caulobacter as an expression system for producing random libraries of peptides or gene fragments for display and panning purposes. The methodologies known in the art for expression of heterologous peptides within an S-layer monomer followed by assembly and adherence of hybrid S-layer protein on a Caulobacter cell surface may now be used in a bacterial-mediated library display system. This has significant advantages over conventional phage display, notably because Caulobacter are of a sufficient size to be sorted through use of conventional cell sorting techniques such as fluorescent activated cell sorting (FACS). Such techniques cannot be used for sorting phage.

This invention provides an isolated Caulobacter deficient in a protease native to Caulobacter that cleaves hybrid Caulobacter S-layer protein monomers. Also provided is a library of such Caulobacter in which members of the library differ by the amino acid sequence of heterologous peptides in hybrid S-layer protein monomers expressed by the members.

This invention also provides a method of producing a Caulobacter optimized for use as a host cell for expression of a hybrid Caulobacter S-layer protein monomer, comprising: i) providing a Caulobacter which exhibits protease activity whereby hybrid S-layer protein monomers expressed by the Caulobacter are cleaved; ii) mutating the Caulobacter; and iii) selecting and culturing a mutated Caulobacter which does not exhibit said activity. Mutation may be by insertion, deletion, or substitution and may be performed through use of radiation and/or chemical mutagens, transposon insertion, homologous recombination or other methods. Also provided are mutated Caulobacter or descendents thereof produced by this method and libraries of such Caulobacter.

The native Caulobacter protease cleaves hybrid S-layer protein monomers as defined herein, in preference to wild-type S-layer protein monomers. The protease appears to be specific for S-layer protein monomers. Within this context, the protease appears to have general specificity for cleavage of hybrid S-layer protein monomers, but tends to cleave C-terminal of Arg and Phe residues. The protease may comprise one or more RTX sequences characteristic of known calcium binding consensus sequences and metalloprotease active site comprising a sequence characteristic of a metalloprotease active site consensus sequence. In this specification, the native Caulobacter protease is termed “Sap”, an acronym for “S-layer associated protease”. In this specification, a gene encoding this protease is termed “sap”.

The Sap protease may comprise a C-terminal portion of about 150 to about 250, preferably about 190 to about 230, and more preferably about 200 amino acids having about 30% or more sequence identity to a portion of the amino acid sequence of a Caulobacter S-layer protein monomer, as determined using the Blast™ search algorithm at default settings (see: Altschul, S. F., et al. 1997). The protease may comprise from about 600 to about 700 amino acids, preferably about 630 to about 670 amino acids, and more preferably about 650 to about 660 amino acids, depending upon the source strain. Sap protease sequences described herein have about 658 amino acids. The portion of a Caulobacter S-layer protein monomer to which the protease exhibits sequence identity will be of similar size to the protease C-terminal portion and will be located toward the N-terminus of the S-layer protein monomer. A portion of an S-layer protein monomer exhibiting sequence identity as described above includes amino acids 23-242 of RsaA. A region of the protease exhibiting such sequence identity to RsaA may be a region corresponding to amino acids 451-650 of the specific Sap amino acid sequence described herein. The protease may further comprise an N-terminal region exhibiting about 50% or more sequence identity (determined as described above) with a P. aeruginosa alkaline protease region, as described below. The protease may comprise an amino acid sequence that has about 75%, 80%, 85%, 90%, 95% or more sequence identity to the specific Sap amino acid sequence disclosed herein.

This invention provides Caulobacter in which a native protease as described above is not expressed or is inactive (a “protease-negative” strain). These Caulobacter may comprise a mutated gene or coding region for the native protease. Protease-negative strains of this invention may also comprise recombinant DNA operably linked to a promoter recognized by Caulobacter, wherein the recombinant DNA comprises a nucleic acid sequence encoding at least a C-terminal secretion signal of Caulobacter S-layer protein monomer. The recombinant DNA may further comprise a nucleic acid sequence encoding sufficient part of Caulobacter S-layer protein monomer N-terminal region to provide for attachment of the coding product of the recombinant DNA to the cell surface of the Caulobacter. The recombinant DNA may comprise substantially all of a Caulobacter S-layer protein gene. The DNA may further comprise restriction sites to facilitate insertion of DNA encoding one or more peptides (including polypeptides and proteins) heterologous to Caulobacter S-layer protein into the recombinant DNA whereby the recombinant DNA encodes a hybrid S-layer protein monomer comprising all or part of an S-layer protein monomer and the one or more heterologous peptides. The recombinant DNA may further comprise DNA encoding a peptide, polypeptide, or protein heterologous to Caulobacter S-layer protein monomer. The recombinant DNA may be present in the Caulobacter on a plasmid or integrated into the Caulobacter genome.

This invention provides a panel or library of Caulobacter wherein individual members of the panel or library express different heterologous peptides, polypeptides, or proteins as part of a hybrid S-layer protein monomer, as described above. Preferably, the Caulobacter in the panel or library will be one or more protease-negative strains of this invention. Also provided are methods of sorting such a library according to whether a target to which the library is exposed binds to hybrid S-layer protein monomers on members of the library.

This invention also provides methods for detecting binding of a target compound to the surface of a Caulobacter that is a member of a library or panel as described above. Preferably, the target compound will be labelled, preferably with a fluorescent label. Detection of members of the panel or library to which the compound is bound may be done by FACS and performed by a flow cytometer. These methods may further comprise selection of Caulobacter to which the target binds, amplification of DNA encoding the heterologous peptide, polypeptide, or protein and sequencing of said DNA.

This invention provides a method of sorting members of a Caulobacter library according to ability of S-layer on a Caulobacter to bind to a target, wherein members of the library express and secrete different hybrid S-layer protein monomers, comprising: i) exposing the library to a fluorescent labelled target; and ii) segregating members of the library with a flow cytometer according to whether the labelled target is bound to a member or is not bound to a member.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: a schematic diagram of the “proteolytic phenotype” associated with the expression of full-length RsaA hybrid proteins.

FIG. 2: a schematic representation of plasmids containing Tn5 interruptions of DNA encoding the Caulobacter protease (Sap).

FIG. 3: a schematic showing location and orientation of Tn5 insertion in the protease (sap) gene of C. crescetus JS4020 and nucleotide sequencing of the Tn5 interrupted gene. Arrows indicate regions of Caulobacter DNA subjected to nucleotide sequencing in plasmids pTZ19Up 1, 4 and 7. Abbreviations for restriction sites: Bm: BamHI; Bg: Bg/II; P: PstI; X: XbaI.

FIG. 4: a copy of a SDS-PAGE gel showing analysis of RsaA(485/IHNVG20) synthesized by Sap⁺ and Sap⁻ strains of C. crescentus. The protein was extracted from the cell-surface by the “low-pH” method. The region of the gels containing the 26 kDa fragment is not shown. A. Proteolytic cleavage of RsaA and RsaA (485/IHNVG20) in Sap⁺ JS4000. Lanes: 1, Low pH extract of JS4000; 2, Low pH extract of (pWB9KSAC:rsaAΔP[485/IHNVG20]); 3, Low pH extract of JS4000 (pWB9KSAC:rsaAΔP). B. Proteolytic cleavage of RsaA (485/IHNVG20) in Sap⁺ JS4020 and Sap⁻ Tn5 mutant JS4021. Lanes: 1, JS4020; 2, JS4021;3, JS4021 (pBBR1MCS:Kmsap). C. Complementation of the UV/NTG mutation in Sap⁻ JS4015 containing either pWB9KSAC:rsaAΔP or pWB9KSAC:rsaAΔP [485/IHNVG20]). Lanes: 1, Cleavage of RsaA (485/IHNVG20) in Sap⁻ JS4015; 2, Cleavage of RsaA in Sap⁻ JS4015; 3, Cleavage of RsaA (485/IHNVG20) in Sap⁺ JS4015 (pBBRIMCS:Kmsap); 4, Cleavage of RsaA in Sap⁺ JS4015 (pBBR1MCS:sap).

FIG. 5: a copy of a SDS-PAGE gel showing analysis of RsaA and RsaA carrying large heterologous inserts synthesized by Sap⁺ strain JS4000 and Sap⁻ strain JS4015. The proteins were extracted from the cell surface using the “low-pH” method. A. RsaA with the insertion of a 3X tandemly repeated P. aeruginosa pilin epitope. A 3-fold tandem repeat of the pilin tip adhesin epitope from a Type IV pilus of P. aeruginosa was prepared and inserted at a position in rsaA corresponding to amino acid 723 of RsaA, using methods as described in Umelo-Njaka, et al. (2000). The total length of this insertion was 134 amino acids. Lanes: 1, JS4000 (pWB9KSAC:rsaAΔP) (a no insertion control); 2, JS4000 (pWB9KSAC:rsaAΔP (723/3X Pilin12); 3, JS4015 (pWB9KSAC:rsaAΔP (723/3XPilin12). B. RsaA with the insertion of a salmonid virus glycoprotein segment. A 112 amino acid segment of the VP2 surface glycoprotein of infectious pancreatic necrosis virus (IPNV) strain SP (16) was prepared by reverse transcriptase mediated PCR, using genomic RNA derived from the virus. The segment was inserted at a position corresponding to amino acid 723 of RsaA using methods similar to those described in Bingle, et al. (1997a) and Simon, et al. (2001) for the insertion of IHNV-G amino acid sequences into RsaA. Lanes: 1, JS4000 (pWB9KSAC:rsaAΔP); 2, JS4000 (pWB9KSAC:rsaAΔP(723/VP2C); 3, JS4015 (pWB9KSAC:rsaAΔP (723/VP2C).

DETAILED DESCRIPTION OF THE INVENTION

In this specification, the terms “S-layer protein monomer” and “S-layer protein” refer to a protein typically expressed by wild-type Caulobacter and which forms an S-layer on the cell surface of the Caulobacter. Representative of these S-layer protein monomers is RsaA, the S-layer protein monomer of C. crescentus. The amino acid sequence of RsaA is known and is also shown in Table 1 (SEQ ID NO: 1). The latter sequence may serve as a reference for identifying S-layer protein monomers of different strains and species of Caulobacter or as a reference for identifying the Caulobacter protease described herein through sequence comparison. The numbering of amino acid residues of RsaA referred to herein corresponds to the residue numbering in Table 1. The sequence of the native gene encoding RsaA is known and is termed “rsaA”. TABLE 1 RsaA amino acid sequence (SEQ ID NO: 1; Genbank Accession No. AAC38665). The rsaA gene sequence is at Genbank Accession No. AF062345. 1 MAYTTAQLVT AYTNANLGKA PDAATTLTLD AYATQTQTGG LSDAAALTNT LKLVNSTTAV 61 AIQTYQFFTG VAPSAAGLDF LVDSTTNTND LNDAYYSKFA QENRFINFSI NLATGAGAGA 121 TAFAAAYTGV SYAQTVATAY DKIIGNAVAT AAGVDVAAAV AFLSRQANID YLTAFVRANT 281 PFTAAADIDL AVKAALIGTI LNAATVSGIG GYATATAAMI NDLSDGALST DNAAGVNLFT 241 AYPSSGVSGS TLSLTTGTDT LTGTANNDTF VAGEVAGAAT LTVGDTLSGG AGTDVLNWVQ 301 AAAVTALPTG VTISGIETMN VTSGAAITLN TSSGVTGLTA LNTNTSGAAQ TVTAGAGQNL 361 TATTAAQAAN NVAVDGGANV TVASTGVTSG TTTVGANSAA SGTVSVSVAN SSTTTTGAIA 421 VTGGTAVTVA QTAGNAVNTT LTQADVTVTG NSSTTAVTVT QTAAATAGAT VAGRVNGAVT 481 ITDSAAASAT TAGKIATVTL GSFGAATIDS SALTTVNLSG TGTSLGIGRG ALTATPTANT 541 LTLNVNGLTT TGAITDSEAA ADDGFTTINI AGSTASSTIA SLVAADATTL NISGDARVTI 601 TSHTAAALTG ITVTNSVGAT LGAELATGLV FTGGAGADSI LLGATTKAIV MGAGDDTVTV 661 SSATLGAGGS VNGGDGTDVL VANVNGSSFS ADPAFGGFET LRVAGAAAQG SHNANGFTAL 721 QLGATAGATT FTNVAVNVGL TVLAAPTGTT TVTLANATGT SDVFNLTLSS SAALAAGTVA 781 LAGVETVNIA ATDTNTTAHV DTLTLQATSA KSIVVTGNAG LNLTNTGNTA VTSFDASAVT 841 GTGSAVTFVS ANTTVGEVVT IRGGAGADSL TGSATANDTI IGGAGADTLV YTGGTDTFTG 901 GTGADIFDIN AIGTSTAFVT ITDAAVGDKL DLVGISTNGA IADGAFGAAV TLGAAATLAQ 961 YLDAAAAGDG SGTSVAKWFQ FGGDTYVVVD SSAGATFVSG ADAVIKLTGL VTLTTSAFAT 1021 EVLTLA

In this specification, the word “protease” with reference to Caulobacter means the native protease disclosed in this specification which cleaves hybrid S-layer protein monomers. This protease exhibits sequence similarity to Caulobacter S-layer protein monomer and presence of the protease may be detected by determining whether a modified S-layer monomer produced by a Caulobacter exhibits the “proteolytic phenotype” described herein. Absence of the protease (or absence of the protease activity) may be similarly determined by absence of or loss of the proteolytic phenotype.

In this specification, the terms “isolated” or “isolate” with reference to a microorganism refers to a naturally occurring or recombinant microorganism substantially free of microorganisms of another genotype or phenotype. As such, the term includes, but is not limited to a microorganism purified from a natural source.

In this specification, the term “peptide” refers to a peptide of two or more amino acids and thus, the term is used interchangeably with the terms “polypeptide” and “protein”. The terms “heterologous peptide” and “passenger peptide” as used throughout this specification with reference to an S-layer protein monomer or gene refers to a sequence of amino acids or a nucleic acid encoding such a sequence of amino acids not found in S-layer protein monomer.

Throughout this specification, the term “restriction site” means a nucleic acid sequence that is recognized by a nuclease whereby the nuclease cleaves a nucleic acid in which the restriction site is located.

In this specification, the terms “library” and “panel” mean a collection or plurality of similar microorganisms, nucleic acids, or peptides with individual members (or groups of members) of the panel or library comprising a feature that is unique to that member or group of members. An example would be a collection of nucleic acids, each one of which comprises a portion encoding a detectable peptide signal with individual members or groups of members in the collection comprising nucleic acid sequences that encode unique peptides. Another example is a collection of recombinant Caulobacter, each of which is capable of expression of a recombinant S-layer protein monomer with the S-layer protein monomer expressed by individual members or groups of members in the collection comprising different peptides heterologous to S-layer protein monomer.

In this specification, the word “modified” with respect to a Caulobacter S-layer monomer refers to a non-wild type S-layer protein monomer. Such a modified monomer may contain deletions, additions, or substitutions as compared to a wild-type monomer. A modified monomer includes one differing in sequence from a wild-type monomer by as few as one amino acid as a result of the introduction of a restriction site into a gene encoding the monomer. The term “hybrid” as applied to Caulobacter S-layer protein monomers refers to a modified S-layer monomer comprising one or more peptides heterologous to Caulobacter S-layer monomers. The term “full-length hybrid” with respect to modified S-layer monomer has the meaning as set out above with respect to the background art.

In this specification, the term “native” refers to a microorganism that is in the form by which it naturally occurs, or with reference to a product of a microorganism, refers to a product that naturally occurs in a microorganism.

In this specification, the word “conservative” with respect to an amino acid substitution refers to the substitution of one amino acid for another at a given location in the peptide, where the substitution can be made without any appreciable loss or gain of function, to obtain a biologically equivalent polypeptide. In making such changes, substitutions of like amino acid residues can be made on the basis of relative similarity of side-chain substituents, for example, their size, charge, hydrophobicity, hydrophilicity, and the like, and such substitutions may be assayed for their effect on the function of the peptide by routine testing. Conserved amino acid substitutions may be made where an amino acid residue is substituted for another having a similar hydrophilicity value (e.g. within a value of plus or minus 2.0), where the following hydrophilicity values are assigned to amino acid residues (as detailed in U.S. Pat. No. 4,554,101, incorporated herein by reference): Arg (+3.0); Lys (+3.0); Asp (+3.0); Glu (+3.0); Ser (+0.3); Asn (+0.2); Gln (+0.2); Gly (0); Pro (−0.5); Thr (−0.4); Ala (−0.5); His (−0.5); Cys (−1.0); Met (−1.3); Val (−1.5); Leu (−1.8); Ile (-1.8); Tyr (−2.3); Phe (−2.5); and Trp (−3.4). Conserved amino acid substitutions may also be made where an amino acid residue is substituted for another having a similar hydrophobic index (e.g., within a value of plus or minus 2.0). In such embodiments, each amino acid residue may be assigned a hydrophobic index on the basis of its hydrophobicity and charge characteristics, as follows: Ile (+4.5); Val (+4.2); Leu (+3.8); Phe (+2.8); Cys (+2.5); Met (+1.9); Ala (+1.8); Gly (−0.4); Thr (−0.7); Ser (−0.8); Trp (−0.9); Tyr (−1.3); Pro (−1.6); His (−3.2); Glu (−3.5); Gln (−3.5); Asp (−3.5); Asn (−3.5); Lys (−3.9); and Arg (−4.5). Conserved amino acid substitutions may also be made where an amino acid residue is substituted for another in the same class, where the amino acids are divided into non-polar, acidic, basic and neutral classes, as follows: non-polar: Ala, Val, Leu, Ile, Phe, Trp, Pro, Met; acidic: Asp, Glu; basic: Lys, Arg, His; neutral: Gly, Ser, Thr, Cys, Asn, Gln, Tyr.

Protease-negative strains of Caulobacter according to this invention may be obtained by mutating Caulobacter using known methodologies, including those described herein, and selecting mutated bacteria which do not express the protease or in which the protease is not active. Activity of the protease may be readily determined using the methodologies described herein. It may also be possible to identify and isolate naturally occurring strains of Caulobacter which may not produce the protease, for example by screening different strains of the bacteria for presence of the metalloprotease activity or for presence of polynucleotides homologous to the Caulobacter native polynucleotides encoding the protease.

Protease-negative Caulobacter of this invention may now be obtained through mutation of Caulobacter by making use of the information herein pertaining to the nucleic acid sequence of sap (Table 2; SEQ ID NO: 2) or the amino acid sequence of Sap (Table 3; SEQ ID NO: 3). This sequence information may be employed to construct a plasmid comprising a mutant sap for homologous recombination with native sap in a selected Caulobacter to cause the native gene to be disrupted. The suicide vectors disclosed herein may be used in the construction of such a plasmid. Alternatively, known methods for site-directed mutagenesis or for introduction of a gene encoding a sap antisense sequence may be employed to produce a protease-negative Caulobacter. TABLE 2 Caulobacter genome sequence containing sap (SEQ ID NO: 2; Genbank Accession No. AY064211). The gene is at nt 186-2326 with the −35 signal at nt 186-191, the Shine-Delgarno ribosomal binding site at nt 247-252 and the coding sequence at nt 258-2234. 1 catttgaaaa ccctttttct acgaaagtcg cggacccgac atcttgcctg ggacctgcag 61 cacaaacgcg ccatgcgagc atttagctgt ggcgcctggg caacaaagtg agttggaagc 121 tgaaaaaggt gacgaaggcc accccgccaa ggtctggctc cgcccgagcg agcgctgtgc 181 gaacttgtcg caaatagcca agattgcaga agaaattctg cttctccata ctcctttcag 241 gtgagtggag cgcgtcggtg tgtagtcagt gcgagcggta tggactgaac ctccacgggg 301 atgatgtcgc cccggccgtc tcgggtggcg agggtcccta cgcgtttgtc gacgccgact 361 tgctgcgcag cgagccgggc tggtcgaacc agttcctggt ccccgcgacc gtgacctatg 481 cgttccgcgc gaccgcaccg gcgagcatgc ccagcgatac gggcggcttt tcgcagttca 541 acgccgccca gatcctccag gccgagaagg cgctgcaggc ctggtccgac gtcgccaaca 601 tcacctttgt ccgcgtgggc cagggcacgt cgggcgaggc cgcctacagc gacaacgcct 661 cgatcctgtt cgccaatttc agcaccggca gcgagggctc ggcgggcttc gcctactatc 721 cgggcaaccc tgcggccagc agccggtccg gcgatgtctg gatcaagtcg acggccggct 781 acaacaccaa cccgaccggc tccaactatg gcggcatggt gctggttcac gagctggggc 841 acgccatcgg catcgcccac cccagcgagt acaacgccag cgccgacgac accctgacct 901 atgcggtcaa cgcgacctac taccaggaca gccgccagta cacggtaatg tcctatttca 961 gcgaggccaa caccggcggc tcgttcggcg gcgcctacgc ctcctcgccc ctgctcgatg 1021 acatcgccgc cgcccagttg gcctatggcg ccaacatgac cacgcgcacc ggcgacacgg 1082 tgtacggctt caactcgacc gccggccgcg agtggttcgc ggcgacctcg tcctcgaccc 1141 ggctggtgtt cgcggtctgg gacgccggcg gcgtcgacac cctggacttc tccggctatc 1201 gcgtggccca gaccatcgac ctgcgagcag gctatttctc cagcgtcggc ggcctgaagg 1261 gcaatgtcac catcgccatg aacgcggtga tcgagaacgc catcggcggc tcggcggccg 1321 acaccatcaa cggaaacgct gtcgacaacc ggctgaccgg cggcgcgggc gccgacatcc 1381 tggacggcgg ccggggcgtc gacaccgccg tcttctccgg cgcctacggc aactacaccc 1441 tgaccgccgc cacgaacggc gcctggtcgg tgctcgaccg ggtggggacg gacgccaccg 1501 ataccctggc gaacatcgag ttcctggcct ttaccgatcg gaccgtgacg ctcgtcgaca 1561 gccgcgtcgc gaccgcgatc agcaatatcc tgcgcctgca gaccttcagc gcctcggccg 1621 aaccgctgtc caagagcctg gcggcctcga tggccgccgg cgccagccat agcgacgcca 1681 tcggccaggt gtccaagacc gcgctgtcga ccagcggggt ggcggtgctg gcctatcagt 1741 tcttcaccgg caagacgccc acggcggccg gcatggatta tctggtcaat ccggacggcg 1801 tgaacgccaa caacctcaac agcgcctact atcagtcgtt caatctcgag aaccgctaca 1861 tcaacttcgc ggtcaatctg ggcaagatcg gcgagggagc caccaagttc ctggccgact 1921 atggcgggct cagcctgttt gacgccacgc gcaaggccta tgcgaccatc tttggcctga 1981 cgcccaccga cgacaaggtg cgcgccctga tcgacggccg caccgactac ttcgccgcct 2041 atggccagga cgggccaaac ggccagggaa ccaaggcggc catggtgggc tggctgatgg 2101 ccgaggcggg caaggccgac atcggcgtct acgccaagtc ggcgggggcc ttcttcgccg 2161 accaggccac caagaatgtc tatggcgtgg atctgatcgg cgtctacgcc aagccggaat 2221 acaacctcat ctgaccgttc gaagggcgcg gcgacaaagg tccagacagc gatttgaagg 2281 gagtaagggc gggcggccct cccccgaaaa ggtcgccgcc cgagttgctt

TABLE 3 Sap amino acid sequence (SEQ ID NO: 3; GenBank accession no. AAL47190) in which underlining indicates a metalloprotein active- site having consensus sequence HEXXHXUGUXH (SEQ ID NO: 4) in which X represents an arbitrary amino acid and U is a bulky hydrophobic residue (Baumann, et al. 1993). The sequences double-underlined indicate Ca⁺² binding sites having consensus sequence GGXGXD (SEQ ID NO: 5) where X is an arbitrary residue (Baumann, et al. 1993). 1 MCSQCERYGL NLHGDDVAPA VSGGEGPYAF VDADSRVGTV DGKKSLTVPE AALQLLRSEP 61 GWSNQFLVPA TVTYAFRATA PASMPSDTGG FSQFNAAQIL QAEKALQAWS DVANITFVRV 121 GQGTSGEAAY SDNASILFAN FSTGSEGSAG FAYYPGNPAA SSRSGDVWIK STAGYNTNPT 181 GSNYGGMVLV HELGHAIGIA HPSEYNASAD DTLTYAVNAT YYQDSRQYTV MSYFSEANTG 241 GSFGGAYASS PLLDDIAAAQ LAYGANMTTR TGDTVYGFNS TAGREWFAAT SSSTRLVFAV 301 WDAGGVDTLD FSGYRVAQTI DLRAGYFSSV GGLKGNVTIA MNAVIENAIG GSAADTINGN 361 AVDNRLTGGA GADILDGGRG VDTAVFSGAY GNYTLTAATN GAWSVLDRVG TDATDTLANI 421 EFLAFTDRTV TLVDSRVATA ISNILRLQTF SASAEPLSKS LAASMAAGAS HSDAIGQVSK 481 TALSTSGVAV LAYQFFTGKT PTAAGMDYLV NPDGVNANNL NSAYYQSFNL ENRYINFAVN 541 LGKIGEGATK FLADYGGLSL FDATRKAYAT IFGLTPTDDK VRALIDGRTD YFAAYGQDGP 601 NGQGTKAAMV GWLMAEAGKA DIGVYAKSAG AFFADQATKN VYGVDLIGVY AKPEYNLI

Protease-negative Caulobacter strains of this invention may be used according to known methodologies to express heterologous peptides within an S-layer protein monomer or as a C-terminal hybrid protein in which a heterologous peptide is attached to a C-terminal secretion signal of the S-layer protein. In this way, unwanted cleavage of the modified or hybrid S-layer gene product is minimized.

Protease-negative Caulobacter for use as an expression system according to this invention will comprise at least a Caulobacter S-layer protein C-terminal secretion signal operably linked to a promoter capable of expression in Caulobacter. This DNA construct may also comprise DNA encoding sufficient N-terminal part of Caulobacter S-layer protein or monomer to provide for adherence of the S-layer protein to the cell surface, once the protein is secreted from the cell. The construct may comprise DNA encoding substantially all of a Caulobacter S-layer protein or protein monomer in which the coding sequence is interrupted by insertion of heterologous DNA. In any case, the heterologous DNA in the construct may be one or more restriction sites to facilitate insertion of further heterologous DNA and/or the heterologous DNA may comprise DNA encoding a peptide, polypeptide, or protein heterologous to Caulobacter S-layer protein.

Extensive information is available for making Caulobacter/S-layer expression systems intended to express full-length hybrid proteins which are displayed on the cell surface (Bingle, et al. [1997(b)]; and, Umelo-Njaka, E., et al. [2000]), including selection of suitable Caulobacter hosts and construction of plasmids suitable for replication in both E. coli and Caulobacter which may be used for expression of hybrid S-layer protein monomers from the host Caulobacter. Preferred Caulobacter hosts do not have a functional native S-layer protein monomer gene and instead express only S-layer protein monomer as directed by recombinant DNA that is either plasmid borne or integrated into the bacterial genome.

Preferred sites for insertion of heterologous DNA sequences into S-layer encoding DNA to produce full-length hybrid proteins have been previously published and may also be determined according to methodologies known in the art. Use of protease-negative strains may make available additional sites since the coding product is not subject to degradation by the metalloprotease.

Caulobacter is particularly suited for display of foreign peptides in view of the wide variety of peptides that may be expressed as part of the S-layer protein and the high copy number of foreign peptide that can be displayed per unit area of the bacterial surface. Successful insertions may be displayed at a number as high as about 20,000-40,000 copies per cell. This allows for very high sensitivity and screening and the ability to look for affinity binding interactions. In comparison, conventional phage display is often limited to one copy number per phage particle, particularly with peptides over about 10-15 amino acids in length. Also, since Caulobacter are capable of forming spontaneous, monolayer biofilms, for certain applications in the area of peptide/protein library screening, the ability to readily attach bacterial cells to a surface at high density will be useful. This facilitates handling of a library of modified cells and for controlling exposure of test compounds to the modified cells.

Preparation of Presentation Libraries Using Caulobacter

In this method, a plasmid containing all or sufficient part of an S-layer protein monomer gene to provide for secretion and adherence of the S-layer monomer is employed. Preferably, the plasmid will contain substantially all of the S-layer coding region and at least one pair of restriction sites to be used for direct oriented cloning of DNA fragments into the S-layer gene. Preferably, these sites will be located at a preferred position in the S-layer coding region demonstrated to be a permissible site for insertion of heterologous material. This can be determined according to preferred sites described in the art or by positioning other peptides at that site and determining whether the peptide is available for antibody binding and does not disrupt secretion, assembly, and attachment of the S-layer array. For example, unique BamH1 restriction sites may be installed by linker mutagenesis as described in PCT patent application published under WO 97/34000. At these sites, one may then install a short set of oligonucleotides which would modify the sites to contain other restriction sites, for example a NcoI and a PstI site in a selector order. The plasmid vector is preferably one that replicates both in Caulobacter as well as another system such as E. coli to facilitate amplification of clones showing a positive result when presented to a target compound. A suitable plasmid may be those previously described which contain a promoter recognized by Caulobacter and into which the S-layer gene may be placed. For example, such a vector is pWB9 as described by Bingle, et al. (1997a). Preferably, the Caulobacter employed for presentation of the library will be a protease-negative strain as described herein.

To produce a library, oligonucleotides may be synthesized to contain known sequences flanking a variable sequence. The known sequences may be required for proper digestion or ligation at restriction sites and for hybridization to primers for polymerase extension reactions. The middle region of the oligonucleotide may be prepared by instructing a DNA synthesizer to vary all four bases at each position. After synthesis, an oligonucleotide complementary to one end may be added and using a polymerase reaction, a double-stranded version provided. The double-stranded DNA may be digested with appropriate restriction enzymes (e.g. NcoI and PstI) making the oligonucleotides ready to be cloned into the corresponding receptor sites of the S-layer gene on the plasmid. This may be done by a ligation reaction and the plasmids then electroported en masse into Caulobacter cells using previously described techniques. All resulting colonies may be pooled and stored in a freezer until required for screening.

An advantage in using protease-negative host Caulobacter is in preparation and screening of large libraries of inserts into the S-layer. These could result from construction of combinatorial peptide libraries (achieved via random or semi-random synthesis of oligonucleotides [and subsequent cloning into the S-layer] that specify peptides, usually of a fixed length of 8-12 amino acids) or for the cloning of random fragments of bacterial genomes or cDNA figments. In such cases minimizing the number of clones that are lost or poorly represented because of cleavage of the insert is important to ensure the maximum probability that clones of utility are contained in the library.

It is typical in the use of such libraries that one is searching for very rare events—those which bind a ligand of interest. If one is searching for vaccine candidates from a genome fragment library the ligand could be an antibody present in sera from patients recovered from an infection. A typical example of an application of combinatorial peptide libraries would be to find peptides that bind to components of a signal transduction cascade to understand the specific interactions that occur. In other cases one may be searching for a peptide sequence that would bind to a molecule of therapeutic value. Thus one could use the peptide as a key component of an affinity matrix that would be used to purify the therapeutic molecule.

Another advantage of S-layer display is that the displaying bacterium is large enough to be readily detected by automated cell sorting methods, including fluorescence-activated cell sorting (FACS). An apparatus for performing FACS is referred to as a “flow cytometer”. In practice one derivatizes a target molecule of interest (i.e. the one for which one expects to find binding peptides in the library) with a fluorescent tag (e.g., fluorescein). One then uses a FACS apparatus to find and segregate the rare library members that bind to the fluorescent tag.

One method of doing so is to use a Bectin-Dickinson FACS machine (model BD FACS Vantage™ TSO SE), equipped with a 50 μm nozzle, using 26 psi of pressure to create a sample stream. The stream is broken into droplets using 40,000 Hz generator. The sample threshold triggered on Fl-1(530/40 nm filter) to exclude non-fluorescent bacteria. This apparatus is able to detect the specific fluorescence of fluorescein and deflect cells displaying a sufficient amount of that label into a collection device thereby segregating the cells. This collection device may be a single tube, to pool all “hits”. The apparatus is also capable of allowing individual cells (“hits” ) to be directed to individual wells of a standard 96 well microtiter plate. These wells would contain culture medium, enabling outgrowth of the individual sorted cells for long-term storage and later experiments.

FACS methodology to identify clones in Caulobacter operates much faster than the prevalent alternative technologies such as library display of peptides on bacteriophage. It is practical to consider examination of a Caulobacter library by the above methods in 1-2 hours. After FACS is performed, one would grow a quantity of the cells that have been diverted as “hits” by adding culture medium. Samples of the cultured cells may be lysed and the plasmid DNA subjected to DNA sequencing. An oligonucleotide known to hybridize to the flanking region of the variable sequence may be employed with a polymerase in a thermocycler apparatus to amplify the region of interest to facilitate sequence determination. The sequence of individual clones will be read and evaluated. Desired clones may be retrieved from replicate samples.

EXAMPLES

Bacterial Strains and Plasmids

Bacterial strains and plasmids are listed in Tables 4 and 5. Escherichia coli strains were grown at 37° C. in Luria-Bertani (LB) medium. When required, antibiotics were included in LB medium at the following concentrations: streptomycin (Sm), 50 μg/ml, kanamycin (Km), 50 μg/ml, ampicillin (Ap), 50 μg/ml, gentamycin 30 μg/ml and chloramphenicol (Cm), 20 μg/ml.

C. crescentus was grown at 30° C. peptone-yeast extract (PYE) medium (0.2% peptone, 0.1% yeast extract, 0.01% CaCl₂, 0.02% MgSO₄, 1.2% agar). When required, antibiotics were included in PYE medium at the following concentrations: streptomycin (Sm), 50 μg/ml, kanamycin (Km), 50 μg/ml, and chloramphenicol (Cm) 2 μg/ml.

Solidified LB and PYE medium was prepared by adding agar to a final concentration of 1.2% w/v. TABLE 4 Bacterial Strains Strain Relevant Characteristics Source/Reference Escherichia coli DH5α recA⁻, endA⁻ Life Technologies Burlington, ON Canada S-17 λ pir recA⁻, Sm^(R), Km^(R) carries λ pir prophage De Lorenzo, et al. (1993) Caulobacter JS4000 RsaA⁻ mutant of C. crescentus strain CB2 Smit and Agabian (1984) (ATCC 15252) JS4020 Strain JS4000 with plasmid pTZ18U; rsaAΔP (485/IHNVG20) integrated into its chromosome JS4021 Sap⁻ Tn5 mutant of strain JS4000 JS4015 Sap⁻ UV/NTG mutant of strain JS4000

TABLE 5 Plasmids Plasmid Relevant Characteristics Reference pG8 Source of IHNV-G gene, Ap. Xu, et al. (1991) pHP45Ω Source of the HindIII fragment Fellay, et al. (1987) carrying the Sm^(R) gene for construction of pTZ18USm pHP45Ω-Km Source of the HindIII fragment Fellay, et al. (1987) carrying the Km^(R) gene for construction of pBBR1MCS: kmsap pAG408 Suicide vector for Tn5 mutagenesis; Suarez, et al. (1997) ColE1, Gm, Km, Ap. pBBR1MCS Broad-host range cloning/expression Kovach, et al. (1994) vector; Cm. pBSK, pBSKII Phagemid cloning/expression vectors; Stratagene, La Jolla CA ColE1, Ap. pTZ18U, Phagemid versions of pUC18 and Amersham Life Sciences pTZ19U pUC19 (Yanisch-Perron, et al. 1985); Mississauga, ON Canada gene expression driven by E. coli lac promoter; ColE1, Ap. pTZ18UB pTZ18U lacking a BamHI site; the Bingle, et al. (1997a) BamHI site was destroyed by BamHI digestion, polishing with PolIK and religation: Ap. pTZ18USm pTZ18U with a Sm^(R) gene inserted as a PolK polished HindIII fragment to the ScaI site of the Ap^(R) gene; Sm. pWB9KSAC Expression vector derived from Bingle, et al. (1997a) pKT215 (Bagdarsian, et al., 1981) incorporating the rsaA promoter; Cm, Sm. pWB9KSAC: A promoterless version of the rsaA Bingle, et al. (1997a) rsaAΔP gene (rsaAΔP) in pWBKSAC; Cm, Sm. pUC9CXS pUC9 (Vieira and Messing, 1982) with Bingle, et al. (1997a) a modified multiple cloning site, Ap, Cm; used to provide DNA fragments with suitable BamHI termini for inframe insertion into BamHI linker mutated rsaAΔP genes. pTZ18UB: rsaA rsaAΔP carrying a BamHI linker Bingle, et al. (1997b) (AciI485BamHI) insertion at a AciI site corresponding to amino acid 485 of RsaA in pTZ18UB; Ap. pTZ18UB: rsaAΔP carrying a BamHI linker Bingle, et al. (1997b) rsaA (MspI450 insertion at a MspI site corresponding BamHI) to amino acid 450 of RsaA in pTZ18UB; Ap. pTZ18UB: rsaA rsaAΔP carrying a BamHI linker (HindPII insertion at a MspI site corresponding 723BamHI) to amino acid 450 of RsaA in PTZ18UB; Ap. pWB9KSAC: rsaAΔP carrying a DNA insert Bingle, et al. (1997b) rsaAΔP encoding 12 amino acids of P. (450/Pilin12) aeruginosa pilin at a position corresponding to amino acid 450 of RsaA in pWB9KSAC. pWB9KSAC: rsaAΔP carrying a DNA insert rsaAΔP encoding tandem 3 copies of pilin (723/3XPilin12) epitope at a position corresponding to amino acid 723 of RsaA in pWB9KSAC. pWB9KSAC: rsaAΔP carrying a DNA insert rsaAΔP encoding amino acids 145-257 of the (723/VP2C) VP2 glycoprotein of IHNV at a protein corresponding to amino acid 723 of RsaA in pWB9KSAC. pTZ18UB/pWBK rsaAΔP carrying a DNA insert SAC: rsaAΔP encoding 20 amino acids of IHNV-G at (485/IHNVG20) a position corresponding to amino acid 485 of RsaA in pTZ18UB or pWBSAC. pTZ18UB/pWBK rsaAΔP carrying a DNA insert SAC: rsaAΔP encoding 20 amino acids of IHNV-G at (450/IHNVG20) a position corresponding to amino acid 450 of RsaA in pTZ18UB or pWBSAC. pTZ18Usm: rsaAΔP carrying a DNA insert rsaAΔP encoding 20 amino acids of IHNV-G at (485/IHNVG20) a position corresponding to amino acid 485 of RsaA in pTZ18Usm. pBBR1MCS: pBBR1MCS with 2 fragments inserted Kmsap into its multiple cloning site (MCS): (1) a 2.2-kb HindIII/BamHI fragment carrying the sap gene and (2) a 1.5-kb HindIII fragment carrying a Km^(R) gene. The orientation of fragment (1) allows expression of the sap gene from either its native promoter or the lac promoter of pBBR1MCS; Cm, Km. pBBR1MCS: sap Equivalent to pBBR1MCS: Kmsap without the 1.5-kb fragment (2). Recombinant DNA Methods

Chromosomal DNA was isolated from Caulobacter using standard methods (Sambrook, et al., 1989), while plasmid DNA was isolated from E. coli and or Caulobacter using the boiling method (RSF1010-based plasmids; Holmes and Quigley, 1981) or the alkaline lysis method (all other plasmids; Birnboim and Doly, 1979). Plasmid DNA was introduced into E. coli and Caulobacter by electroporation as described by Gilchrist and Smit (1991).

DNA-modifying enzymes were purchased from Life Technologies (Burlington, ON, Canada) or New England Biolabs (Mississauga, ON, Canada) and were used according the manufacturer's instructions.

Agarose gel electrophoresis (Tris-Borate-EDTA buffer) was conducted by standard methods (Sambrook, et al., 1989); in preparative applications, DNA fragments were purified using QIAEX II (Qiagen Inc., Chatsworth, Calif.).

Southern hybridization was done using standard methodologies (Sambrook, et al., 1989; and, Taso, et al., 1983). DNA samples were electrophoresed on a 0.8% agarose gels and probed with oligonucleotides labeled with {α-32P} dCTP (Amersham) using the Rediprime II™ random prime labeling system (Amersham Pharmacia Biotech, UK).

Polymerase chain reaction (PCR) amplification was conducted by using TaqI or Pfx DNA polymerase (Life Technologies, Burlington, ON, Canada) according to manufacturer's instructions and a Techne Progene™ Thermal Cycler (Mandel Scientific Co., Guelph, ON, Canada).

Nucleotide sequencing was performed on an ABI PRISMTM™ 377 automated sequencer. Oligonucleotides were synthesized using a Perkin-Elmer ABI synthesizer.

Isolation of RsaA

Wild-type S-Jayer protein (RsaA) and full-length RsaA hybrid proteins were isolated from Caulobacter cells by low-pH extraction (Walker, et al. 1992; and, Nomellini, et al. 1997). Mid log phase cells (OD₆₀₀ of 0.5 to 1.0) were washed once in 10 mM HEPES buffer, pH=7.2 by centrifugation (10,000×g, 5 min) and then resuspended by vortexing in 100 mM HEPES buffer, pH 2.0 equivalent to 5% of the original culture volume. After 5 min at room temperature, the cells were pelleted by centrifugation and the supernatant fluid containing RsaA was recovered.

SDS-PAGE and Western Analysis

SDS-PAGE was conducted by the discontinuous gel method of Laemmli (1970); samples were treated at 37° C., rather than boiling, in SDS-PAGE sample buffer prior to electrophoresis (Smit and Agabian, 1984). Western immunoblot analysis was carried out as described by Walker, et al. (1994) using an anti-RsaA polyclonal antibody as a probe. Antibody binding was visualized using goat anti-rabbit or mouse serum coupled to horse-radish peroxidase and colour-forming reagents. Before analysis of low-pH extracted RsaA by SDS-PAGE, 2 μL of 1 N NaOH was added per 20 μL of extracted protein.

Western colony immunoblotting (Bingle, et al. 1997b) was performed by spread plating cells on PYE agar to a density of approximately 100-200 cfu's per standard Petri plate. Following incubation for 3-4 days at 30° C., nitrocellulose membranes were pressed onto surface of the plates for 2 min. The membranes with adherent colonial material were then lifted-off, allowed to air dry for 5-10 min, blocked with 5% skim milk and finally processed as above.

Amino Terminal Sequence Determination

Protein samples for N-terminal sequencing were electrophoretically transferred from SDS-PAGE gels to a 0.2 μm PVDF membrane (Bio Rad) using a BioRad transfer apparatus according to the manufacturer's instructions. The membrane was briefly stained in Coomassie blue R-250 (Sigma) destained in 50% methanol and air dried. The desired protein band was excised from the membrane using a scalpel and the N-terminal amino acid sequence was obtained by automated Edman degradation.

Construction of Strain JS4020

A sample of plasmid pTZ18USm:rsaΔP(485/IHNVG20) was electroportated into the Sm sensitive, RsaA⁻ strain: JS4000. The resulting cell suspension was plated on solid PYE medium containing 50 μg/mL of Sm to select for cells containing the chromosomally integrated plasmid resulting from a single cross-over event between the plasmid borne copy of rsaA and the chromosomal copy of rsaA in strain JS4000. Sm resistant (SM^(R)) cells from several colonies were then screened by low-pH extraction for the presence of cell-surface bound S-layer protein fragments characteristic of proteolytic cleavage within the IHNV-G insert as well as proteolytic cleavage within the RsaA N-terminus (the “proteolytic phenotype”; see FIG. 1). One isolate exhibiting both Sm-resistance and the expected proteolytic pattern was retained and designated stain JS4020.

Tn5 Mutagenesis of JS4020

Conjugation was used to introduce a Tn5 derivative carried by the suicide vector pAG408 into JS4020. 100 μL of an overnight culture of E. coli S-17 λ pir (pAG408) was mixed with 1 mL of an early log phase culture of JS4020 in 5 mL of 10 mM MgSO₄. The cell mixture was collected on a sterile 22 mm diameter nitrocellulose filter paper and the filter paper was placed on the surface of PYE agar in a petri dish. After overnight incubation at 30° C., the cells were dislodged from the filter in 5 mL of 10 mM MgSO₄ and 100 μL aliquots were plated on PYE agar containing 50 μg/mL each of Km and Sm.

UV/NTG Mutagenesis of JS4000

A mutant pool of strain JS4000 previously created by ultraviolet (UV) light mutagenesis (Ong, C., et al. [1990] was further mutagenized using nitrosoguanidine (NTG) according to the method of Miller (1972).

Characterization of Caulobacter Protease

As reported in Bingle, et al. (1997b), insertion of a 12 amino acid peptide derived from aeruginosa pilin at centrally-located positions in the full-length 1026 amino acid RsaA primary sequence often results in cleavage of the hybrid protein within the pilin-peptide insert and/or at a site distant from the insertion site within the N-terminus of RsaA. Cleavage within the pilin peptide insert yields 2 fragments which remain bound to the cell surface while cleavage within the RsaA N-terminus yields a 26 kDa N-terminal cleavage product which remains surface-bound, and a C-terminal fragment which is released into the growth medium (FIG. 1). For the purposes of this specification, cells exhibiting the proteolytic phenomena shown in FIG. 1 are said to possess the “proteolytic phenotype”.

Using conventional techniques, we determined that Caulobacter exhibits a protease activity that is not energy dependent (ATP does not stimulate the activity); the protease activity occurs free inside the cell and is not associated with cell membranes or the periplasm of this Gram negative organism; EDTA is somewhat inhibitory (a characteristic of metalloproteases); there is no induction of the enzyme stimulated by the presence of a recombinant S-layer protein shown to be cleaved; and, there is an absence of other cell proteins being affected by the protease, when it is degrading a recombinant S-layer protein. Insertions which result in consistent cleavage of a recombinant product tend to be in the central {fraction (2/3)} of the S-layer coding region, with sites near the N or C-terminal regions tending to be safe from protease effects. This information, coupled with the sequence information described below indicates that the protease attaches to the monomer and has a limited range along the length of the protein to act upon. The C-terminal region is needed as a secretion signal for the S-layer protein, and the N-terminal region is needed for attachment of the S-layer protein assembly to the cell surface.

C. crescentus (strain CB2A) was treated with ultraviolet light or chemical mutagens as described above, at rates permitting about 1% cell survival. Individual cells surviving the mutagenesis received a plasmid version of the S-layer gene containing a heterologous insertion shown to be efficiently cleaved according to the proteolytic phenotype. Colonies were then screened using an immunoblot method involving overlaying the colony with a nitrocellulose disk followed by removal of the disk and treatment with S-layer protein-specific antibodies in a manner essentially the same as used in Western-Blot method. A typical result is a “halo” of antibody reactivity surrounding the colony, due to the cleavage of the monomer which then prevents it from assembling into a crystallized, surface-attached S-layer. Colonies that fail to produce a halo are rare and these were selected for subsequent confirmation that they lacked the ability to cleave the recombinant S-layer molecule in the manner seen by wild-type cells.

Characterization of Proteolysis of IHNV-G Peptide Inserts

In order to confirm that the proteolytic phenotype is not associated with just pilin peptide inserts, a 20 amino acid vaccine epitope (ASESREELLEAHAEIISTNS; SEQ ID NO: 6) derived from amino acids 306 to 325 of the infectious hematopoietic necrosis virus glycoprotein (IHNV-G) was inserted at 2 permissive sites corresponding to amino acids 485 and 450 in RsaA. The IHNV-G DNA insert was synthesized by PCR, inserted into rsaAΔP and introduced into the RsaA⁻ strain: JS4000, using the Caulobacter expression plasmid pWB9KSCAC by methodology identical to that described for pilin peptide DNA in Bingle, et al (1997a).

Despite the difference in the nature of the insert, RsaA hybrid proteins carrying INHV-G peptide insertions (100 kDa) exhibited the same proteolytic phenotype (FIG. 1) as cells synthesizing RsaA molecules carrying pilin peptide inserts. Insertion of the 20 amino acid IHNV-G peptide at either amino acid 485 or 450, resulted in the cleavage of the hybrid protein within the peptide insert yielding 2 50 kDa fragments, consistent with cleavage within the IHNV-G insert (FIG. 4A), as well as the surface-bound 26 kDa fragment. Native RsaA (98 kDa) was not subjected to cleavage (FIG. 4A).

N-terminal microsequencing revealed that the cleavage of INHV-G insert occurred between an Arg and Ser residue. This cleavage site was not located within the IHNV-G peptide itself but rather in the portion encoded by the 3′ fusion joint between IHNV-G DNA and rsaA DNA, as was the case for pilin peptide insertions.

Tn5 Mutagenesis of JS4020

When proteolytic cleavage of a RsaA hybrid protein occurs at an N-terminal site distant from the site of the heterologous insertion, the C-terminal cleavage product fragment is shed from the cell surface. In colony immunoblots probed with RsaA antibody, this shed RsaA fragment yields an immunoreactive halo around colonies. Tn5 mutagenesis leading to the loss of the proteolytic phenotype may be detected by screening for loss of this halo around colonies using colony immunoblot technique.

Strain JS4020 was used as a background to detect the loss of the proteolytic phenotype as the result of Tn5 mutagenesis. This strain possesses a chromosomal copy of rsaA carrying a DNA insert encoding the 20 amino IHNV-G peptide at a site corresponding to RsaA amino acid 485.

Tn5 mutagenesis of strain JS4020 was conducted as described above and the resulting mutants were subjected to colony immunoblot assays. To confirm the loss of the proteolytic phenotype and to screen out Tn5 insertions in rsaA or components of its secretion apparatus, cells from colonies showing halo loss were further screened for the presence of the undegraded RsaA/IHNVG hybrid protein using the low-pH extraction method coupled with SDS-PAGE.

Isolation of Tn5 Interrupted Chromosomal DNA

Three mutants of JS4020 clearly exhibiting loss of the proteolytic phenotype were isolated. Chromosomal DNA was prepared from all three mutants, digested with BamHI and BglII and subjected to Southern analysis using the 1.5 kb KpnI (Tn5) fragment from pAG408 used as a probe. Because the Tn5 derivative in pAG408 possesses single BamHI and BglII sites which occur at opposite ends of the Tn5, single DNA fragments will result from digestion of the Tn5 interrupted chromosomal DNA with either BamHI or BglII separately but together the two fragments would include the 5′ and 3′ portion of the interrupted region in addition to Tn5.

Relevant BglII and BamHI Tn5-tagged fragments (from digests of chromosomal DNA of all 3 mutants) were recovered from agarose gels for propagation in the BamHI site of pBSK(−). For one of the mutants, a 6 kb BamHI fragment and a 7 kb BglII fragment were successfully cloned yielding plasmids pEU1 and pEU2 respectively. The transposable region of pAG408 is 2.2 kb in length. Thus, about 4 kb and 5 kb of DNA flanking Tn5 was made available for nucleotide sequence analysis. Using the appropriate known restriction sites from pAG408 as a guide in conjunction with restriction mapping, DNA immediately flanking the Tn5 was excised from pEU1 and pEU2 and inserted into pTZ19U, yielding plasmids pTZ19UP1 and pTZ19UP7 (FIG. 2) which were sequenced.

Nucleotide Sequencing of DNA Flanking the Tn5 Insertion Site

Nucleotide sequence information from pTZ19UP1 and pTZ19UP7 concerning the DNA immediately flanking the Tn5 insertion site was used to search the nucleotide sequence of the genome of C. crescentus strain CB15 in the Institute for Genomic Research (TIGR) database (Nierman, et al. 2001). As a result, an open-reading frame of 1977bp initiating with GTG (gene CC0746, GenBank accession no. AE005750) was identified, which when translated, provides an N-terminal region which exhibits significant sequence similarity to several metalloproteases: most notably the alkaline protease of Pseudomonas aeruginosa (Okuda, K., et al. [1990]).

Although the nucleotide sequence contained in the TIGR database was derived from analysis of the C. crescentus genome and this example concerns JS4000 derived from strain CB2, the open reading frames initially compared between the two strains shows that the two putative protease genes (collectively termed “sap” herein) are almost identical at the nucleotide sequence level and that the TIGR sequence can be used as a guide for sequencing of the DNA flanking the Tn5 insertion site. In addition, this sequence comparison revealed both the probable orientation of the Tn5 insertion and that the insertion site was located almost exactly in the centre of the gene with approximately 1000 bp on either side of the insertion site (FIG. 3).

Using this information and the TIGR sequence as a guide to the location of suitable restriction sites, one additional pTZ19U-based plasmid, pTZ19UP4, was constructed (FIGS. 2 and 3). Using each of pTZ19U 1, 4 and 7, the nucleotide sequence encompassing 1000 bp on either side of the Tn5 insertion mutation associated with loss of the proteolytic phenotype was assembled. The sap DNA sequence and Sap amino acid sequence so derived are shown in Tables 2 and 3 above.

Analysis of Sap Sequence

The nucleotide sequence of the JS4000 sap gene (Table 2) differed by only 2 base pairs from that reported by Nierman, et al. (2001) for strain CB15. Both predict a primary translation product of 658 amino acid residues, but sequence for the JS4000 gene indicates a valine at position 217 (Table 3) while the nucleotide sequence of the reported CB15 sap gene predicts a conservative substitute (alanine) at this position. Thus, the sap gene and Sap protein for these strains are interchangeable. The congruence between the sap nucleotide sequences of strains JS4000 and CB15 extended both upstream into a putative gene encoding an OmpA-like protein and downstream into a GC-rich region with the potential to code for a stem-loop structure. These regions of DNA exhibited 100% nucleotide sequence identity between the two strains. A -35 transcription initiation signal (5′-TTGTCG-3′) and a translation initiation signal (5′-GGAG-3″) characteristic of C. crescentus housekeeping genes (Malakooti, J., et al. [1995]) were also identified in these regions of both strains.

The amino acid sequence of Sap can be divided into two regions, each of which show significant similarity to other proteins in the National Center for Biotechnology (NCBI) protein database as identified using the BLAST algorithm in conjunction with the default parameters.

The N-terminal region of Sap exhibits significant similarity to the alkaline metalloprotease (AprA) of P. aeruginosa (and other members of this family of proteases). Specifically, amino acids 89-417 of Sap (Table 3) have about 55% sequence identity to amino acids 92-408 of AprA. This region of the Sap protein contains the metalloprotease active site consensus sequence (HEXXHXUGUXH; SEQ ID NO: 4) as well as 4 of the 7 Ca⁺² binding consensus sequences (GGXGXD; SEQ ID NO: 5) found in AprA (also known as “RTX sequences”).

The C-terminal region of Sap exhibits significant similarity to the N-terminal region of the C-terminally truncated 358 amino acid mutant S-layer protein of C. crescentus JS4000 as well as the N-terminal region of the wild-type S-layer proteins such as those from C. crescentus strains CB15 and NA1000. Specifically, amino acids 451-650 of Sap (Table 3) have about 33% sequence identity to amino acids 23-242 of RsaA (see Table 6). No other amino acid sequence in the NCBI protein database showed any significant degree of sequence similarity to the C-terminal region of Sap. Two regions of the Sap amino acid sequence show little or no similarity to sequences in the NCBI protein database: the extreme N-terminus (amino acids 1-88) and the region covering amino acids 418-540. If Sap was functionally equivalent to AprA, this region of the protein would contain a C-terminal Type I secretion signal (which is absent in Sap). The extreme N-terminal region of Sap lacks any apparent signal leader peptide and the Sap protein does not appear to contain transmembrane domains. These features indicate that Sap is localized to the cytoplasm. TABLE 6 Sequence comparison of amino acids 451-650 of Sap (SEQ ID NO: 3) to amino acids 23-242 of RsaA (SEQ ID NO: 1) with identical and similar (+) residues shown. SAP451 SASAEPLSKSLAASMAAGASHSDAIGQVSKTALSTSGVAVLAYQFFTGKTPTAAGMDYLV 510 +A+   L      +   G S + A+    K   ST+ VA+  YQFFTG  P+AAG+D+LV RSA23 AATTLTLDAYATQTQTGGLSDAAALTNTLKLVNSTTAVAIQTYQFFTGVAPSAAGLDFLV 82 SAP511 NPDGVNANNLNSAYYQSFNLENRYINFAVNLGK-IGEGATKFLADYGGLSLFDATRKAYA 569 +    N N+LN AYY  F  ENR+INF++NL    G GAT F A Y G+S       AY RSA83 D-STTNTNDLNDAYYSKFAQENRFINFSINLATGAGAGATAFAAAYTGVSYAQTVATAYD 141 SAP570 TIFGLTPTD-------------------DKVRALIDGRTDYFAAYGQDGPNGQGTKAAMV 610   I G                       D + A +   T + AA   D       KAA++ RSA142 KIIGNAVATAAGVDVAAAVAFLSRQANIDYLTAFVRANTPFTAAADID----LAVKAALI 197 SAP611 GWLMAEAGKADIGVYAKSAGAFFAD-----QATKNVYGVDLIGVY 650 G ++  A  + IG YA +  A   D      +T N  GV+L   Y RSA198 GTILNAATVSGIGGYATATAAMINDLSDGALSTDNAAGVNLFTAY 242 Isolation of a Protease Deficient, Mutant in a UV/NTG Mutant Library of JS4000

In order to create a Sap− mutant lacking a Tn5 insertion, a pool of UV/NTG mutagenized JS400× was transformed with pWBKSAC:rsaA(485/IHNVG20) and screened for loss of the proteolytic phenotype (FIG. 4B). Screening of approximately 20,000 colonies resulted in the identification of 3 mutants lacking the proteolytic phenotype. One was selected and designated JS4015.

Complementation analysis was used to confirm that the UV/NTG induced mutation was located in the sap gene. JS4015 was transformed with pBBR1MCS:Kmsap (a broad host range plasmid compatible with pWBKSAC) carrying a PCR amplified copy of the sap gene from JS4000. PCR primers were chosen to amplify a sequence 140 bp upstream and downstream of the sap coding region to capture the native promoter of the sap gene. When pBBR1MCS:Kmsap was introduced into JS4015, the proteolytic phenotype was restored (FIG. 4C). The Tn5 mutation in strain JS4020 was also complemented in the same way using pBBR1MCS:sap.

Sequence analysis of PCR amplified DNA from the JS4015 sap gene indicates several scattered base changes caused by the combined NTG and UV mutagenesis. Of particular interest is a change of two adjacent bases resulting in the substitution of a Lysine residue for Val₁₈₈ of Sap, very near the protease active site.

To ensure that the phenotype of Sap⁻ JS4015 is not simply related to IHNV-G insertions, several other full-length RsaA hybrid protein constructs known to be affected by degradation were tested. The results for two are shown in FIG. 5. In all instances significant degradation of the hybrid full-length rsaA protein occurred in a wild-type host (JS4000) while none was detected in the Sap⁻ JS4015 strain.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of skill in the art in light of the teachings of this invention that changes and modification may be made thereto without departing from the spirit or scope of the invention as recited in the attached claims. All patents, patent applications, and references referred to herein are hereby incorporated by reference.

References

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1. An isolated Caulobacter deficient in a protease native to Caulobacter that cleaves hybrid Caulobacter S-layer protein monomers.
 2. The isolated Caulobacter of claim 1, wherein said protease comprises a metalloprotease active site.
 3. The isolated Caulobacter of claim 1 or 2, wherein said protease comprises one or more RTX sequences.
 4. The isolated Caulobacter of claim 1, wherein said protease comprises a C-terminal portion having a first sequence of about 150 to about 250 amino acids, the first sequence having 30% or more sequence identity to a second sequence of about 150 to about 250 amino acids, the second sequence being an N-terminal portion of a Caulobacter S-layer protein monomer.
 5. The isolated Caulobacter of claim 4, wherein the first and second sequences independently have about 190 to about 230 amino acids.
 6. The isolated Caulobacter of claim 4, wherein the second sequence is amino acids 23 to 242 of SEQ ID NO:
 1. 7. The isolated Caulobacter of claim 6, wherein the first sequence is about 200 amino acids in length.
 8. The isolated Caulobacter of claim 1, wherein said protease comprises an amino acid sequence having about 75% or more sequence identity to SEQ ID NO:
 3. 9. The isolated Caulobacter of claim 8, wherein the identity to SEQ ID NO: 3 is about 80% or more.
 10. The isolated Caulobacter of claim 8, wherein the identity to SEQ ID NO: 3 is about 85% or more.
 11. The isolated Caulobacter of claim 8, wherein the identity to SEQ ID NO: 3 is about 90% or more.
 12. The isolated Caulobacter of claim 8, wherein the identity to SEQ ID NO: 3 is about 95% or more.
 13. The isolated Caulobacter of claim 1, wherein said protease comprises an amino acid sequence substantially identical to SEQ ID NO: 3 or a sequence in which one or more amino acids of SEQ ID NO: 3 are conservatively substituted.
 14. The isolated Caulobacter of claim 1, wherein said protease comprises SEQ ID NO:
 3. 15. The isolated Caulobacter according to claim 1, wherein the isolated Caulobacter is deficient in the protease as a result of a deletion, substitution, or addition of nucleotide in a gene encoding the protease.
 16. The isolated Caulobacter of claim 1, wherein the isolated Caulobacter is incapable of secreting an S-layer protein monomer encoded by a gene native to the Caulobacter.
 17. The isolated Caulobacter of claim 16, wherein the isolated Caulobacter comprises a recombinant DNA capable of expression of an S-layer protein monomer.
 18. The isolated Caulobacter of claim 17, wherein the S-layer monomer expressed by the recombinant DNA is a hybrid S-layer protein monomer.
 19. The isolated Caulobacter of claim 18, wherein the hybrid S-layer protein monomer is secreted by the isolated Caulobacter, is capable of attachment to a cell surface of the Caulobacter, and comprises one or more peptides heterologous to Caulobacter S-layer protein monomer.
 20. A library of Caulobacter in which members of the library are different isolated Caulobacter according to claim 19, wherein the members differ by amino acid sequence of the one or more heterologous peptides.
 21. A method of sorting a library of claim 20 according to ability for a heterologous peptide to bind to a target, comprising exposing the library to the target, and separating members of the library that bind to the target from members which do not bind to the target.
 22. The method of claim 21, wherein the target is labelled and presence of the label bound to a member is indicative of binding of the target to the member.
 23. The method of claim 22, wherein the label is fluorescent and the separation is performed by a flow cytometer.
 24. A method of producing a Caulobacter optimized for use as a host cell for expression of a hybrid Caulobacter S-layer protein monomer, comprising: i) providing a Caulobacter which exhibits protease activity whereby hybrid S-layer protein monomers expressed by the Caulobacter are cleaved; ii) mutating the Caulobacter; and iii) selecting and culturing a mutated Caulobacter which does not exhibit said activity.
 25. The method of claim 24, wherein the Caulobacter is mutated by introduction into the Caulobacter of a nucleic acid capable of homologous recombination with all or part of SEQ ID NO:
 2. 26. The method of claim 24, wherein the Caulobacter is mutated by transposon insertion.
 27. The method of claim 24, wherein the Caulobacter is mutated by one or more of radiation and a chemical mutagen.
 28. The method of claim 24, wherein the Caulobacter which exhibits protease activity expresses a protein comprising an amino acid sequence having about 75% or more sequence identity to SEQ ID NO: 3, and the Caulobacter is mutated so as to result in insertion, deletion, or substitution of at least one amino acid in said amino acid sequence.
 29. A mutated Caulobacter or descendents thereof, produced by the method of claim
 24. 30. A library of mutated Caulobacter or descendents thereof of claim 29, wherein members of the library express and secrete different hybrid Caulobacter S-layer protein monomers.
 31. A method of sorting a library of claim 30 according to ability for the different hybrid S-layer protein monomers to bind a target, comprising exposing the library to the target, and separating members of the library that bind to the target from members which do not bind to the target.
 32. The method of claim 31, wherein the target is labelled and presence of the label bound to a member is indicative of binding of the target to the member.
 33. The method of claim 32, wherein the label is fluorescent and the separation is performed by a flow cytometer.
 34. A method of sorting members of a Caulobacter library according to ability of S-layer on a Caulobacter to bind to a target, wherein members of the library express and secrete different hybrid S-layer protein monomers, comprising: i) exposing the library to a fluorescent labelled target; and ii) segregating members of the library with a flow cytometer according to whether the labelled target is bound to a member or is not bound to a member. 